[Chimera-users] Input from Avogadro, solvation.

Paul Buscemi busce004 at umn.edu
Sat May 20 15:02:12 PDT 2017



Dear Chimera,

Three basic questions:

I’m using Avogadro to construct my models and import as mol2 or pdb types. I often obtain messages as



or  that the atom is not “listed” .  

Is there a preparation I can use for transfer of models ? Alternatively do  you suggest any other program to construct models ?

2) If I use Tools to solvate a model,  should I use the “Start solvate tool” under MD and/or check “Periodic Boundary Conditions.


3) Im considering building a multicore system  ( two 16 core Xeon’s)  as a 64 bit system would Chimera take advantage of the multi-core system ?
Would the upgrade funds be better spent on memory ?

Regards,

Paul Buscemi,
UMN BICB
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